chr18-57545828-A-AG
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000140.5(FECH):c.*4883_*4884insC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00627 in 152,252 control chromosomes in the GnomAD database, including 15 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0063 ( 15 hom., cov: 32)
Consequence
FECH
NM_000140.5 3_prime_UTR
NM_000140.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.35
Genes affected
FECH (HGNC:3647): (ferrochelatase) The protein encoded by this gene is localized to the mitochondrion, where it catalyzes the insertion of the ferrous form of iron into protoporphyrin IX in the heme synthesis pathway. Mutations in this gene are associated with erythropoietic protoporphyria. Two transcript variants encoding different isoforms have been found for this gene. A pseudogene of this gene is found on chromosome 3.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 18-57545828-A-AG is Benign according to our data. Variant chr18-57545828-A-AG is described in ClinVar as [Likely_benign]. Clinvar id is 327329.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.051 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FECH | NM_000140.5 | c.*4883_*4884insC | 3_prime_UTR_variant | 11/11 | ENST00000262093.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FECH | ENST00000262093.11 | c.*4883_*4884insC | 3_prime_UTR_variant | 11/11 | 1 | NM_000140.5 | |||
FECH | ENST00000652755.1 | c.*4883_*4884insC | 3_prime_UTR_variant | 11/11 |
Frequencies
GnomAD3 genomes AF: 0.00622 AC: 947AN: 152134Hom.: 15 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00627 AC: 954AN: 152252Hom.: 15 Cov.: 32 AF XY: 0.00729 AC XY: 543AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Protoporphyria, erythropoietic, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at